Merge branch 'master' into stable

environment.yaml

@@ -2,9 +2,9 @@ name: rptools
 channels:
   - conda-forge
 dependencies:
-  - python >=3.9
+  - python <=3.11
   - brs_utils # rpcompletion, rpfba, Args
-  - cobra # rpfba, rpextractsink, rplibs
+  - cobra >=0.26.3 # rpfba, rpextractsink, rplibs
   - timeout-decorator # rpextractsink
   - rdkit # rpextractsink, rplibs
   - python-libsbml # rplibs, rpfba
@@ -13,13 +13,12 @@ dependencies:
   - scipy # rpthermo
   - equilibrator-api # rpthermo
   - equilibrator-cache >=0.5.4 # rpthermo
-  - openbabel # rpthermo (equilibrator-assets)
   - colored # rplibs
   - networkx >=2.5 # rplibs
   - filetype  # rplibs (conda-forge)
-  - rr_cache>=3.1.1 # rpcompletion
+  - rr_cache >=3.1.1 # rpcompletion
   - rxn_rebuild # rpcompletion
   - chemlite # rpcompletion ,rpfba, rpthermo
   - h5py # rpscore
   - xgboost # rpscore
-  - sqlalchemy =1.4.31 # (for pandas requirements)
+  - bs4 # rpviz

rptools/rprank/__init__.py

@@ -4,4 +4,4 @@
 @author: Joan Hérisson, Jean_Loup Faulon
 """
 
-from .rprank import rank
+from rptools.rprank.rprank import rank

rptools/rprank/__main__.py

@@ -1,16 +1,5 @@
-from typing import (
-    Dict,
-    List
-)
-from logging import (
-    Logger,
-    getLogger
-)
-from os import (
-    path as os_path,
-    makedirs
-)
-from .rpRank import rank
+from os import path as os_path
+from .rprank import rank
 from .Args import add_arguments
 from rptools.rplibs import rpPathway
 from rptools import build_args_parser